20 Pull requests merged by 5 people

• [CI] switch off autosyncing of labels

  #4895 merged Jan 22, 2025

• Transfer of fasteners dependency to filelock

  #4800 merged Jan 12, 2025

• Exclude automated formatting PRs from git blame

  #4886 merged Jan 10, 2025

• [fmt] Format all

  #4885 merged Jan 8, 2025

• [fmt] core

  #4874 merged Jan 8, 2025

• update Python versions gh-ci-cron.yaml

  #4845 merged Jan 7, 2025

• Refine pep8speaks

  #4877 merged Jan 6, 2025

• Addition of water selection documentation

  #4881 merged Jan 6, 2025

• DocFix: Added the documentation for run() method in polymer.rst

  #4864 merged Jan 6, 2025

• Implementation of WaterSelection for water resiude selection

  #4854 merged Jan 3, 2025

• [fmt] utils, import, viz tests

  #4875 merged Dec 31, 2024

• [fmt] Format topology module and tests

  #4849 merged Dec 29, 2024

• [fmt] Format analysis module and tests

  #4848 merged Dec 29, 2024

• ENH: support tpx 134 (GMX 2024.4)

  #4866 merged Dec 28, 2024

• [fmt] Coordinates

  #4856 merged Dec 24, 2024

• [fmt] Tests and various folders in MDAnalysis tests

  #4857 merged Dec 24, 2024

• [fmt] Format everything but package and testsuite

  #4859 merged Dec 24, 2024

• [fmt] Guesser

  #4851 merged Dec 24, 2024

• [fmt] Selections

  #4861 merged Dec 24, 2024

• Add pep8speaks configuration

  #4858 merged Dec 24, 2024

11 Pull requests opened by 6 people

• Enable parallelization for analysis.polymer

  #4871 opened Dec 28, 2024

• WIP, ENH: add TPR position and velocity read support

  #4873 opened Dec 29, 2024

• Bump the github-actions group across 1 directory with 4 updates

  #4876 opened Jan 1, 2025

• Fix broken links from MDanalysis Docs

  #4882 opened Jan 5, 2025

• Unpin parmed w/ numpy v2

  #4883 opened Jan 7, 2025

• Parallelizes `MDAnalysis.analysis.InterRDF` and `MDAnalysis.analysis.InterRDF_s`

  #4884 opened Jan 7, 2025

• Update Codecov action to v5

  #4887 opened Jan 8, 2025

• [fmt] Format after PR#4800

  #4890 opened Jan 13, 2025

• Preserve Full Trajectory Information in AnalysisBase

  #4892 opened Jan 14, 2025

• Test on smaller pdb for guesser to reduce test duration

  #4893 opened Jan 14, 2025

• Parallelizes `MDAnalysis.analysis.msd`

  #4896 opened Jan 20, 2025

11 Issues closed by 5 people

• Box dimension was read wrongly

  #4897 closed Jan 23, 2025

• [CI] change labeler action to NOT sync labels

  #4840 closed Jan 22, 2025

• replace fasteners

  #4797 closed Jan 12, 2025

• [CI] Update cron matrix

  #4806 closed Jan 7, 2025

• guess_bonds which guessing types

  #2143 closed Jan 7, 2025

• Add contexts to guess attributes better (especially elements and masses)

  #2630 closed Jan 7, 2025

• Is it feasible to convert PCA to UMAP parallel implementation?

  #4865 closed Jan 6, 2025

• Document water selection keyword

  #4880 closed Jan 6, 2025

• [docs] MDAnalysis.analysis.polymer.PersistenceLength does not document run() method

  #4793 closed Jan 6, 2025

• Implementation of Water Selection token

  #4839 closed Jan 3, 2025

• Error: Your tpx version is 134, which this parser does not support, yet

  #4855 closed Dec 28, 2024

3 Issues opened by 3 people

• Preserve Full Trajectory Information in Parallel Analysis

  #4891 opened Jan 13, 2025

• issue with large dcd seeking

  #4879 opened Jan 2, 2025

• Feature proposal: Adding a ResidenceTime Analysis Routine

  #4868 opened Dec 27, 2024

17 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Update PR template after relicensing

  #4860 commented on Jan 17, 2025 • 12 new comments

• distopia 0.3.0 compatibility changes

  #4734 commented on Jan 7, 2025 • 8 new comments

• add `relprop` for atom selection and corresponding UT

  #4841 commented on Jan 7, 2025 • 2 new comments

• Implementing `gemmi`-based mmcif reader (with easy extension to PDB/PDBx and mmJSON)

  #4712 commented on Jan 21, 2025 • 1 new comment

• Implementation of SugarSelection

  #4790 commented on Jan 11, 2025 • 0 new comments

• 'MDAnalysis.analysis.align' parallelization

  #4738 commented on Jan 11, 2025 • 0 new comments

• Limit threads usage in numpy during test to reduce test time

  #4584 commented on Jan 14, 2025 • 0 new comments

• Wrap RDKit drawing code for AtomGroups

  #2900 commented on Jan 18, 2025 • 0 new comments

• `MDAnalysis.analysis.msd`: Implement parallelization or mark as unparallelizable

  #4676 commented on Jan 20, 2025 • 0 new comments

• Adopt a reader for live-streamed Interactive MD (IMD) version 3 trajectories

  #4827 commented on Jan 19, 2025 • 0 new comments

• Explore solutions for codecov upload failures

  #4576 commented on Jan 8, 2025 • 0 new comments

• Make the `AnalysisBase` compatible with live simulation streams

  #4828 commented on Jan 7, 2025 • 0 new comments

• `MDAnalysis.analysis.rdf`: Implement parallelization or mark as unparallelizable

  #4675 commented on Jan 7, 2025 • 0 new comments

• Implement fancy guessers (e.g., force-field aware)

  #598 commented on Jan 7, 2025 • 0 new comments

• Support for numpy.dtypes.StringDType in AtomGroup containers?

  #4847 commented on Jan 6, 2025 • 0 new comments

• check_box and triclinic_vectors don't respect dtype

  #3500 commented on Jan 5, 2025 • 0 new comments

• [CI] tests related to guessers are slow

  #4842 commented on Dec 24, 2024 • 0 new comments